Rethymno has few museums. They are not well adverted nor big but still they have something to show. In Rethymno The Venetian Fortress Fortezza has museums.
The Nekropolis of Armenoi is Minoan cemetery that locates 8 km south of Rethymno. It is a beautiful and peaceful place. Its treasures have been transferred and secured to Archeological Museum of Rethymno which too is a small indoor museum. I recommend you to see both; the nekropolis and museum.
Paleontological Museum definitely is a place you should bring all the LittlePeople who are interested about dinosaurs etc. Again, a very small place but it is sometimes good if you want to educate children to get interested about the museums and history.
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Here are five museums mentioned. Fortezza and Nekropolis of Armenoi can be very hot places but offer a great adventure also for school aged children. If you go to see them, remember to have a flash light to create better adventure! Notice that the prices are not high and they have also reduced fees for students and children get usually free ticket.